Index

A

add_jitter() (in module gensec.precon) add_rank1() (gensec.precon.HessianBuilder method) add_rank1_from_atlist() (gensec.precon.HessianBuilder method) add_to_known() (gensec.known.Known method) add_to_known_coms() (gensec.known.Known method) add_to_known_orientations() (gensec.known.Known method) add_to_known_torsions() (gensec.known.Known method) add_unity() (gensec.precon.HessianBuilder method) align_to_axes() (in module gensec.modules)

all_right() (in module gensec.modules) all_within() (gensec.precon.Bravais method) angle_between() (gensec.known.Known method) (in module gensec.modules) apply_conf() (gensec.structure.Structure method) apply_configuration() (gensec.structure.Structure method) apply_torsions() (gensec.structure.Structure method) ASR() (in module gensec.precon) atoms_object() (gensec.structure.Structure method)

B

BFGS_mod (class in gensec.optimize)

BFGSLineSearch_mod (class in gensec.optimize) Bravais (class in gensec.precon)

C

C12AB() (in module gensec.precon) C6AB() (in module gensec.precon) Calculator (class in gensec.relaxation) canonize() (in module gensec.precon) carried_atoms() (in module gensec.modules) chains() (gensec.precon.Pairs method) check_positive_symmetric() (in module gensec.precon)

clashes_with_fixed_frame() (in module gensec.modules) coms_diff() (gensec.known.Known method) construct_graph() (in module gensec.modules) create_configuration() (gensec.structure.Structure method) create_connectivity_matrix() (in module gensec.modules) create_directory() (gensec.outputs.Directories method) create_torsion_list() (in module gensec.modules) current_dir() (gensec.outputs.Directories method)

D

dd_arccos() (in module gensec.precon) dd_arcsin() (in module gensec.precon) dd_cosv1v2() (in module gensec.precon) dd_cross() (in module gensec.precon) dd_directed_angle() (in module gensec.precon) dd_dot() (in module gensec.precon) dd_mult() (in module gensec.precon)

dd_norm() (in module gensec.precon) dd_normalized() (in module gensec.precon) dd_power() (in module gensec.precon) dd_prod() (in module gensec.precon) dd_sum() (in module gensec.precon) detect_cycles() (in module gensec.modules) detect_rotatble() (in module gensec.modules) Directories (class in gensec.outputs)

E

estimate_mu() (gensec.relaxation.Calculator method) exclude_rotatable_from_cycles() (in module gensec.modules)

ExpHessian() (in module gensec.precon) exponent() (gensec.precon.LindhExponent method) extract_conf_keys_from_row() (gensec.structure.Structure method)

F

find_alpha() (in module gensec.alphas) find_in_database() (gensec.structure.Structure method) find_in_known() (gensec.known.Known method) find_last_dir() (gensec.outputs.Directories method) find_traj() (gensec.known.Known method)

finish_relaxation() (gensec.relaxation.Calculator method) finished() (gensec.outputs.Directories method) (gensec.relaxation.Calculator method) Fixed_frame (class in gensec.structure) func() (in module gensec.alphas)

G

gensec (module) gensec.alphas (module) gensec.coefficients (module) gensec.defaults (module) gensec.known (module) gensec.modules (module) gensec.optimize (module) gensec.outputs (module) gensec.precon (module) gensec.protocols (module)

gensec.relaxation (module) gensec.structure (module) get_internal_vector() (gensec.known.Known method) get_known() (gensec.known.Known method) get_len() (gensec.known.Known method) (gensec.structure.Fixed_frame method) get_pairs() (in module gensec.precon) get_R0AB() (in module gensec.alphas) (in module gensec.precon) getroots() (in module gensec.modules) getvec() (gensec.precon.Pairs method)

H

HessianBuilder (class in gensec.precon)

I

init() (gensec.protocols.Protocol method) insertbreak() (in module gensec.modules)

internal_clashes() (in module gensec.modules) intramolecular_clashes() (in module gensec.modules) isposvec() (in module gensec.precon)

K

Kabsh_rmsd() (in module gensec.precon)

Known (class in gensec.known) known() (gensec.outputs.Directories method)

L

latvec() (gensec.precon.Bravais method) LBFGS_Linesearch_mod (class in gensec.optimize) LindhExponent (class in gensec.precon) LindhHessian() (in module gensec.precon) load_parameters() (in module gensec.outputs)

log() (gensec.optimize.LBFGS_Linesearch_mod method) (gensec.optimize.TRM_BFGS method) (gensec.optimize.TRM_BFGS_IPI method) log_rejected() (gensec.optimize.TRM_BFGS method) (gensec.optimize.TRM_BFGS_IPI method)

M

make_canonical_pyranosering() (in module gensec.modules) makeorthvec() (in module gensec.precon) measure_quaternion() (in module gensec.modules) measure_torsion_of_last() (in module gensec.modules) merge_together() (in module gensec.modules)

min_trm() (gensec.optimize.TRM_BFGS method) (gensec.optimize.TRM_BFGS_IPI method) minimal_angle() (gensec.known.Known static method) model_matrix() (in module gensec.precon) mult_quats() (in module gensec.modules)

N

name2row() (in module gensec.precon)

O

orientational_diff() (gensec.known.Known method)

Output (class in gensec.outputs)

P

Pairs (class in gensec.precon) preconditioned_hessian() (in module gensec.precon)

PreconLBFGS_mod (class in gensec.optimize) produce_quaternion() (in module gensec.modules) Protocol (class in gensec.protocols)

Q

q_bending() (in module gensec.precon) q_bond() (in module gensec.precon)

q_torsion() (in module gensec.precon) quaternion_set() (in module gensec.modules)

R

RAB() (in module gensec.precon) random() (in module gensec.structure) Rcut() (gensec.precon.LindhExponent method) read_configuration() (gensec.structure.Structure method) relax() (gensec.relaxation.Calculator method)

remove_last_directory() (gensec.outputs.Directories method) reset_hessian() (gensec.optimize.LBFGS_Linesearch_mod method) rho_ij() (in module gensec.precon) Rotation() (in module gensec.modules) rotation_quat() (in module gensec.modules) run() (gensec.protocols.Protocol method)

S

save_obj() (in module gensec.alphas) save_to_directory() (gensec.outputs.Directories method) set_centre_of_mass() (in module gensec.modules) set_constrains() (gensec.relaxation.Calculator method) (in module gensec.precon) set_fixed_frame_positions() (gensec.structure.Fixed_frame method)

set_structure_positions() (gensec.structure.Structure method) step() (gensec.optimize.LBFGS_Linesearch_mod method) (gensec.optimize.PreconLBFGS_mod method) (gensec.optimize.TRM_BFGS method) (gensec.optimize.TRM_BFGS_IPI method) Structure (class in gensec.structure)

T

to_array() (gensec.precon.HessianBuilder method) torsional_diff() (gensec.known.Known method) torsions_from_conf() (gensec.structure.Structure method)

translate() (in module gensec.modules) translate_back() (in module gensec.modules) TRM_BFGS (class in gensec.optimize) TRM_BFGS_IPI (class in gensec.optimize)

U

unit_quaternion() (in module gensec.modules) unit_vector() (in module gensec.modules) update() (gensec.optimize.BFGS_mod method) (gensec.optimize.BFGSLineSearch_mod method)

update_BFGS() (gensec.optimize.TRM_BFGS method) update_H() (gensec.optimize.TRM_BFGS method) (gensec.optimize.TRM_BFGS_IPI method)

V

vdW_element() (in module gensec.precon)

vdwHessian() (in module gensec.precon)

W

Workflow (class in gensec.outputs) write_configuration() (gensec.outputs.Output method) write_parameters() (gensec.outputs.Output method)

write_successfull_generate() (gensec.outputs.Output method) write_successfull_relax() (gensec.outputs.Output method) write_to_report() (gensec.outputs.Output method)